Question: Which genes are differentially expressed in different subtypes of cancer
General wokflow
Cleaning procedure
Male-female ratio
We can see that many of the differentially expressed genes are on the left side of the volcano plot.
Here is an analysis of PCA plots showing the scree and cumulative variance explained.


The high dimentionality required to explain 85% of the variablity of the data shows that cancer is a difficult task
Overlapped clustering of patients
The clusters from patients with and without tumor overlap, meaning the PCA is not separating clearly the clusters.